#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 10 ps with a timestep of 1 fs # Temperature 298.2 K #------------------------------------------------------------------------------- # Fix shake is needed for water in pcff+ fix shaken all shake .0001 20 50000 a 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2812 = # of frozen angles find clusters CPU = 0.001 seconds reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo ${Nthermo} thermo 0 fix 1 movable nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 1000 1000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.5_averages.txt off 1 fix 3 movable ave/time 1 1 1 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.5_instantaneous.txt restart 10000 2.5.restart dump sci all custom 1000 2.5.xyz id mol type q xs ys zs group rdfgroup_1 union subset_Li subset_Cl 350 atoms in group rdfgroup_1 compute rdf_1 rdfgroup_1 rdf 200 4 1 fix rdf_1 rdfgroup_1 ave/time 1 100 100 c_rdf_1[*] file 2.5_PairCorrelation_all_1.out mode vector group rdfgroup_2 union subset_Li subset_S 38 atoms in group rdfgroup_2 compute rdf_2 rdfgroup_2 rdf 200 4 9 fix rdf_2 rdfgroup_2 ave/time 1 100 100 c_rdf_2[*] file 2.5_PairCorrelation_all_2.out mode vector group rdfgroup_3 union subset_Li subset_O(SO4) 38 atoms in group rdfgroup_3 compute rdf_3 rdfgroup_3 rdf 200 4 8 fix rdf_3 rdfgroup_3 ave/time 1 100 100 c_rdf_3[*] file 2.5_PairCorrelation_all_3.out mode vector group rdfgroup_4 union subset_Li subset_O(H2O) 2819 atoms in group rdfgroup_4 compute rdf_4 rdfgroup_4 rdf 200 4 7 fix rdf_4 rdfgroup_4 ave/time 1 100 100 c_rdf_4[*] file 2.5_PairCorrelation_all_4.out mode vector group rdfgroup_5 union subset_Li subset_H 2819 atoms in group rdfgroup_5 compute rdf_5 rdfgroup_5 rdf 200 4 2 fix rdf_5 rdfgroup_5 ave/time 1 100 100 c_rdf_5[*] file 2.5_PairCorrelation_all_5.out mode vector group rdfgroup_6 union subset_Na subset_Cl 399 atoms in group rdfgroup_6 compute rdf_6 rdfgroup_6 rdf 200 6 1 fix rdf_6 rdfgroup_6 ave/time 1 100 100 c_rdf_6[*] file 2.5_PairCorrelation_all_6.out mode vector group rdfgroup_7 union subset_Na subset_S 87 atoms in group rdfgroup_7 compute rdf_7 rdfgroup_7 rdf 200 6 9 fix rdf_7 rdfgroup_7 ave/time 1 100 100 c_rdf_7[*] file 2.5_PairCorrelation_all_7.out mode vector group rdfgroup_8 union subset_Na subset_O(SO4) 87 atoms in group rdfgroup_8 compute rdf_8 rdfgroup_8 rdf 200 6 8 fix rdf_8 rdfgroup_8 ave/time 1 100 100 c_rdf_8[*] file 2.5_PairCorrelation_all_8.out mode vector group rdfgroup_9 union subset_Na subset_O(H2O) 2868 atoms in group rdfgroup_9 compute rdf_9 rdfgroup_9 rdf 200 6 7 fix rdf_9 rdfgroup_9 ave/time 1 100 100 c_rdf_9[*] file 2.5_PairCorrelation_all_9.out mode vector group rdfgroup_10 union subset_Na subset_H 2868 atoms in group rdfgroup_10 compute rdf_10 rdfgroup_10 rdf 200 6 2 fix rdf_10 rdfgroup_10 ave/time 1 100 100 c_rdf_10[*] file 2.5_PairCorrelation_all_10.out mode vector group rdfgroup_11 union subset_K subset_Cl 383 atoms in group rdfgroup_11 compute rdf_11 rdfgroup_11 rdf 200 3 1 fix rdf_11 rdfgroup_11 ave/time 1 100 100 c_rdf_11[*] file 2.5_PairCorrelation_all_11.out mode vector group rdfgroup_12 union subset_K subset_S 71 atoms in group rdfgroup_12 compute rdf_12 rdfgroup_12 rdf 200 3 9 fix rdf_12 rdfgroup_12 ave/time 1 100 100 c_rdf_12[*] file 2.5_PairCorrelation_all_12.out mode vector group rdfgroup_13 union subset_K subset_O(SO4) 71 atoms in group rdfgroup_13 compute rdf_13 rdfgroup_13 rdf 200 3 8 fix rdf_13 rdfgroup_13 ave/time 1 100 100 c_rdf_13[*] file 2.5_PairCorrelation_all_13.out mode vector group rdfgroup_14 union subset_K subset_O(H2O) 2852 atoms in group rdfgroup_14 compute rdf_14 rdfgroup_14 rdf 200 3 7 fix rdf_14 rdfgroup_14 ave/time 1 100 100 c_rdf_14[*] file 2.5_PairCorrelation_all_14.out mode vector group rdfgroup_15 union subset_K subset_H 2852 atoms in group rdfgroup_15 compute rdf_15 rdfgroup_15 rdf 200 3 2 fix rdf_15 rdfgroup_15 ave/time 1 100 100 c_rdf_15[*] file 2.5_PairCorrelation_all_15.out mode vector group rdfgroup_16 union subset_Mg subset_Cl 494 atoms in group rdfgroup_16 compute rdf_16 rdfgroup_16 rdf 200 5 1 fix rdf_16 rdfgroup_16 ave/time 1 100 100 c_rdf_16[*] file 2.5_PairCorrelation_all_16.out mode vector group rdfgroup_17 union subset_Mg subset_S 182 atoms in group rdfgroup_17 compute rdf_17 rdfgroup_17 rdf 200 5 9 fix rdf_17 rdfgroup_17 ave/time 1 100 100 c_rdf_17[*] file 2.5_PairCorrelation_all_17.out mode vector group rdfgroup_18 union subset_Mg subset_O(SO4) 182 atoms in group rdfgroup_18 compute rdf_18 rdfgroup_18 rdf 200 5 8 fix rdf_18 rdfgroup_18 ave/time 1 100 100 c_rdf_18[*] file 2.5_PairCorrelation_all_18.out mode vector group rdfgroup_19 union subset_Mg subset_O(H2O) 2963 atoms in group rdfgroup_19 compute rdf_19 rdfgroup_19 rdf 200 5 7 fix rdf_19 rdfgroup_19 ave/time 1 100 100 c_rdf_19[*] file 2.5_PairCorrelation_all_19.out mode vector group rdfgroup_20 union subset_Mg subset_H 2963 atoms in group rdfgroup_20 compute rdf_20 rdfgroup_20 rdf 200 5 2 fix rdf_20 rdfgroup_20 ave/time 1 100 100 c_rdf_20[*] file 2.5_PairCorrelation_all_20.out mode vector timestep 1 run 10000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2557377 grid = 27 27 54 stencil order = 5 estimated absolute RMS force accuracy = 0.0032430487 estimated relative force accuracy = 9.7663448e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8000 2916 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 5 5 13 21 neighbor lists, perpetual/occasional/extra = 1 20 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard (2) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (3) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (4) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (5) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (6) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (7) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (8) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (9) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (10) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (11) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (12) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (13) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (14) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (15) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (16) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (17) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (18) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (19) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (20) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (21) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none SHAKE stats (type/ave/delta/count) on step 0 2 0.97 8.00249e-13 8436 2 103.7 7.07558e-11 2812 Per MPI rank memory allocation (min/avg/max) = 13.91 | 14.07 | 14.18 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 0 1e-06 2228.6687 93962.523 1.2789064 295.33481 44.303622 99.288148 0 0 19656.797 46379.821 -220.49494 -206909.64 -140729.43 5612.1482 10000 10000 1909.2076 93962.523 1.2789064 297.09377 42.509732 88.361914 0 0 19484.648 46435.248 -220.49494 -206911.21 -140860.44 5645.5732 Loop time of 192.583 on 16 procs for 10000 steps with 9188 atoms Performance: 4.486 ns/day, 5.350 hours/ns, 51.926 timesteps/s 99.3% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 77.327 | 83.184 | 92.176 | 41.8 | 43.19 Bond | 0.021642 | 0.052993 | 0.075018 | 7.1 | 0.03 Kspace | 17.544 | 26.588 | 32.514 | 74.4 | 13.81 Neigh | 4.8521 | 4.8544 | 4.8562 | 0.1 | 2.52 Comm | 4.0514 | 4.1479 | 4.2252 | 2.4 | 2.15 Output | 0.015989 | 0.017579 | 0.01924 | 0.8 | 0.01 Modify | 73.152 | 73.247 | 73.327 | 0.6 | 38.03 Other | | 0.4914 | | | 0.26 Nlocal: 574.25 ave 611 max 547 min Histogram: 2 2 0 1 6 3 1 0 0 1 Nghost: 9030.31 ave 9146 max 8902 min Histogram: 1 1 2 3 1 0 2 2 2 2 Neighs: 322536 ave 347975 max 303687 min Histogram: 4 0 1 1 3 4 1 0 1 1 Total # of neighbors = 5160572 Ave neighs/atom = 561.66434 Ave special neighs/atom = 1.9037875 Neighbor list builds = 497 Dangerous builds = 0 undump sci restart 0 dump sci all custom 10000 2.5.xyz id mol type q xs ys zs run 0 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2557377 grid = 27 27 54 stencil order = 5 estimated absolute RMS force accuracy = 0.0032430487 estimated relative force accuracy = 9.7663448e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8000 2916 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 10000 2 0.97 1.4841e-06 8436 2 103.7 0.0001025 2812 Per MPI rank memory allocation (min/avg/max) = 44.43 | 44.59 | 44.7 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 10000 10000 1910.0104 93962.523 1.2789064 297.09377 42.509732 88.361914 0 0 19484.648 46435.248 -220.49494 -206911.21 -140860.44 5645.5732 Loop time of 3.84769e-06 on 16 procs for 0 steps with 9188 atoms 125.1% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Kspace | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 3.848e-06 | | |100.00 Nlocal: 574.25 ave 611 max 547 min Histogram: 2 2 0 1 6 3 1 0 0 1 Nghost: 9030.31 ave 9146 max 8902 min Histogram: 1 1 2 3 1 0 2 2 2 2 Neighs: 322536 ave 347975 max 303687 min Histogram: 4 0 1 1 3 4 1 0 1 1 Total # of neighbors = 5160572 Ave neighs/atom = 561.66434 Ave special neighs/atom = 1.9037875 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute rdf_1 unfix rdf_1 group rdfgroup_1 delete uncompute rdf_2 unfix rdf_2 group rdfgroup_2 delete uncompute rdf_3 unfix rdf_3 group rdfgroup_3 delete uncompute rdf_4 unfix rdf_4 group rdfgroup_4 delete uncompute rdf_5 unfix rdf_5 group rdfgroup_5 delete uncompute rdf_6 unfix rdf_6 group rdfgroup_6 delete uncompute rdf_7 unfix rdf_7 group rdfgroup_7 delete uncompute rdf_8 unfix rdf_8 group rdfgroup_8 delete uncompute rdf_9 unfix rdf_9 group rdfgroup_9 delete uncompute rdf_10 unfix rdf_10 group rdfgroup_10 delete uncompute rdf_11 unfix rdf_11 group rdfgroup_11 delete uncompute rdf_12 unfix rdf_12 group rdfgroup_12 delete uncompute rdf_13 unfix rdf_13 group rdfgroup_13 delete uncompute rdf_14 unfix rdf_14 group rdfgroup_14 delete uncompute rdf_15 unfix rdf_15 group rdfgroup_15 delete uncompute rdf_16 unfix rdf_16 group rdfgroup_16 delete uncompute rdf_17 unfix rdf_17 group rdfgroup_17 delete uncompute rdf_18 unfix rdf_18 group rdfgroup_18 delete uncompute rdf_19 unfix rdf_19 group rdfgroup_19 delete uncompute rdf_20 unfix rdf_20 group rdfgroup_20 delete unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 0:05:27